Maybe the new plot is that you are a hobo who tries living inside different gyms in secret. When the gym leaders find out, you have to make your Pokemon beat up theirs. Eventually you sell enough Pokemon on the Black and White market that you get to buy your own gym! Then all of the previous gym leaders become homeless, and join team Rocket. And that was how Team Rocket was made. :3

nice! i totally suport this XD.
and let's create a light type while we're at it so that when you finish the game said gym leaders don't simply join TR but also fall to the dark side of the pokeforce!
also i think darth vader should be the new champion so you get to have an epic battle using your brand new, shiny light saber... hmm, sorry i mean light type to defeat him.
oh and right before you fight him he could say something like: X, i'm your father... come to the Y side of the pokeforce!
not only would it give us a reason to have a light type, it also would give us a father for the 2nd time in 6 gens!